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strange that there don't have to be mountains in the area for it to be considered mountainnous
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Typically, altitudes on approaches are not adjusted unless the surounding terrain is considered 'precipitous'. The altitude buffer is to allow for localized pressure changes due to wind flowing over terrain.
In the very north lattitudes, cold weather corrections are often made to altitudes on the approach to compensate for the contraction of the pressure levels.
In answer to the above questions,
#1
In theory, only V1 should change. However, if you read part 25, you will see that Vr can depend on V1. You will also see that V2 can depend on Vr in some cases.
So I would say that V1 is directly affected, while Vr and V2 COULD be indirectly affected. Not likely, in my personal opinion.
#2
Well explained by above posts.
And it is true that the max descent gradient from the faf to a point 50 ft above the landing threshold can not exceed 400 ft per nm.
Interestingly, MDA is not considered in this calculation.
Therefore a dawdling descent to MDA could leave you unable to descend normally to the runway. Dive and drive, baby!! (Anticipating flames over this).
#3
Zero-zero is correct